Convert-Pheno

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META.json  view on Meta::CPAN

            "DateTime::Format::ISO8601" : "0.17",
            "Devel::Size" : "0.84",
            "File::ShareDir::ProjectDistDir" : "1.000009",
            "Hash::Fold" : "v1.0.0",
            "JSON::Validator" : "5.14",
            "JSON::XS" : "4.03",
            "JSONLD" : "0.006",
            "Mojolicious" : "9.33",
            "Moo" : "2.005005",
            "Path::Tiny" : "0.144",
            "Sort::Naturally" : "1.03",
            "Term::ANSIColor" : "5.01",
            "Text::CSV_XS" : "1.50",
            "Text::Levenshtein::XS" : "0.503",
            "Text::Similarity" : "0.13",
            "Types::Standard" : "2.004000",
            "XML::Fast" : "0.17",
            "YAML::XS" : "0.88",
            "perl" : "5.026000"
         }
      },

META.yml  view on Meta::CPAN

  DateTime::Format::ISO8601: '0.17'
  Devel::Size: '0.84'
  File::ShareDir::ProjectDistDir: '1.000009'
  Hash::Fold: v1.0.0
  JSON::Validator: '5.14'
  JSON::XS: '4.03'
  JSONLD: '0.006'
  Mojolicious: '9.33'
  Moo: '2.005005'
  Path::Tiny: '0.144'
  Sort::Naturally: '1.03'
  Term::ANSIColor: '5.01'
  Text::CSV_XS: '1.50'
  Text::Levenshtein::XS: '0.503'
  Text::Similarity: '0.13'
  Types::Standard: '2.004000'
  XML::Fast: '0.17'
  YAML::XS: '0.88'
  perl: '5.026000'
resources:
  bugtracker: https://github.com/CNAG-Biomedical-Informatics/convert-pheno/issues

Makefile.PL  view on Meta::CPAN

        'x_contributors' => [],
    },
    PREREQ_PM => {
        'JSON::XS'                       => '4.03',
        'YAML::XS'                       => '0.88',
        'Path::Tiny'                     => '0.144',
        'Term::ANSIColor'                => '5.01',
        'Text::CSV_XS'                   => '1.50',
        'Text::Similarity'               => '0.13',
        'Text::Levenshtein::XS'          => '0.503',        
        'Sort::Naturally'                => '1.03',
        'File::ShareDir::ProjectDistDir' => '1.000009',
        'DBI'                            => '1.643',
        'Moo'                            => '2.005005',
        'DBD::SQLite'                    => '1.72',
        'Mojolicious'                    => '9.33',
        'XML::Fast'                      => '0.17',
        'JSON::Validator'                => '5.14',
        'Types::Standard'                => '2.004000',
         #'Test::Deep'                     => '1.204',
         #'Test::Exception'                => '0.43',

cpanfile  view on Meta::CPAN

# No specific version needed

# bin and lib
requires 'JSON::XS';
requires 'YAML::XS';
requires 'Path::Tiny';
requires 'Term::ANSIColor';
requires 'Text::CSV_XS';
requires 'Text::Similarity';
requires 'Text::Levenshtein::XS';
requires 'Sort::Naturally';
requires 'DBI';
requires 'Moo';
requires 'DBD::SQLite';
requires 'Mojolicious::Lite';
requires 'XML::Fast';
requires 'JSON::Validator';
requires 'IO::Socket::SSL';
requires 'Types::Standard';
requires 'File::ShareDir::ProjectDistDir';
requires 'Data::Leaf::Walker';

lib/Convert/Pheno/IO/CSVHandler.pm  view on Meta::CPAN

package Convert::Pheno::IO::CSVHandler;

use strict;
use warnings;
use autodie;
use feature qw(say);
use File::Basename;
use Text::CSV_XS           qw(csv);
use Sort::Naturally        qw(nsort);
use List::Util             qw(any);
use File::Spec::Functions  qw(catdir);
use IO::Compress::Gzip     qw($GzipError);
use IO::Uncompress::Gunzip qw($GunzipError);

use Data::Dumper;
use Devel::Size qw(total_size);
use Convert::Pheno::IO::FileIO qw(io_yaml_or_json);
use Convert::Pheno::Tabular::REDCap::Dictionary;
use Convert::Pheno::OMOP::Definitions;

lib/Convert/Pheno/IO/FileIO.pm  view on Meta::CPAN

use autodie;
use feature qw(say);
use Path::Tiny;
use File::Basename;
use List::Util qw(any);
use YAML::XS qw(Load Dump);
$YAML::XS::Boolean = 'JSON::PP';    # use JSON::PP::Boolean objects
use JSON::XS;
use IO::Compress::Gzip     qw($GzipError);
use IO::Uncompress::Gunzip qw($GunzipError);
use Sort::Naturally qw(nsort);
use Data::Leaf::Walker;
use Exporter 'import';
our @EXPORT = qw(read_json read_yaml io_yaml_or_json write_json write_yaml);

#########################
#########################
#  SUBROUTINES FOR I/O  #
#########################
#########################